[galaxy-user] Question about Cuffdiff

Hi, I am confused about the first line in cuffdiff (using Galaxy on the cloud, not sure if it's different for local instances). It reads: Transcripts:(choose a file)A transcript GTF file produced by cufflinks, cuffcompare, or other source. What file should I load here? I have 4 groups of 2-4 r

[galaxy-user] Cuffcompare error

Hi, I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets (3 replicates of 2 conditions). I am consistently getting the following error: Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to

[galaxy-user] TopHat/Cufflinks visualization

How do people on this mailing list usually visualize Tophat and/or Cufflinks results (eg. tracks on UCSC browser)? I have only this once before, and I started with a .wig file that I uploaded to the genome browser, however it looks like Tophat does not give any .wig file in the output. Suggestion